Dimensions Affecting Representation Styles in Ontologies

There are different ways to formalise roughly the same knowledge, which negatively affects ontology reuse and alignment and other tasks such as formalising competency questions automatically. We aim to shed light on, and make more precise, the intuitive notion of such `representation styles' through characterising their inherent features and the dimensions by which a style may differ. This has led to a total of 28 different traits that are partitioned over 10 dimensions. The operationalisability was assessed through an evaluation of 30 ontologies on those dimensions and applicable values. It showed that it is feasible to use the dimensions and values and resulting in three easily recognisable types of ontologies. Most ontologies had clearly one or the other trait, whereas some were inherently mixed due to inclusion of different and conflicting design decisions

The Proteasix Ontology

Background: The Proteasix Ontology (PxO) is an ontology that supports the Proteasix tool; an open-source peptide-centric tool that can be used to predict automatically and in a large-scale fashion in silico the proteases involved in the generation of proteolytic cleavage fragments (peptides)Methods: The PxO re-uses parts of the Protein Ontology, the three Gene Ontology sub-ontologies, the Chemical Entities of Biological Interest Ontology, the Sequence Ontology and bespoke extensions to the PxO in support of a series of roles: 1. To describe the known proteases and their target cleaveage sites. 2. To enable the description of proteolytic cleaveage fragments as the outputs of observed and predicted proteolysis. 3. To use knowledge about the function, species and cellular location of a protease and protein substrate to support the prioritisation of proteases in observed and predicted proteolysis.Results: The PxO is designed to describe the biological underpinnings of the generation of peptides. The peptide-centric PxO seeks to support the Proteasix tool by separating domain knowledge from the operational knowledge used in protease prediction by Proteasix and to support the confirmation of its analyses and results.Availability: The Proteasix Ontology may be found at: http://bioportal.bioontology.org/ontologies/PXO . This ontology is free and open for use by everyone